Neck linkers

Kinesin-1 comprises three major domains the N-terminal motor domain that can be subdivided into the core motor domain and the adjacent neck linker and neck region, the central stalk domain, and the C-terminal tail or light chain-binding domain (Fig. 1A). The core motor domain has a length of about 325 amino acids and contains both the microtubule and the nucleotide binding elements. In different kinesin families, this motor... 

The monomeric rat kinesin construct (amino acids 1-354) comprises the head domain (including the core motor domain, amino acids 2-325, and the neck linker, amino acids 326-338) and the first half of the neck domain. In the crystal structure, the neck linker consists of two strands, /19 and /110, that form hydrogen bonds with strands />8 and fJ7 of the core /1-sheet (Fig. 2E). The neck linker ends close to loop L10 at the tip of the core domain where the (a-helical neck domain (helix a7) is attached to the core motor domain. Its orientation is roughly in the plane of the core /1-sheet and perpendicular to the strands. 

Structural Alignment of the Switch-1 and Switch-2 Regions of Kinesin Motor Domains with Secondary Structure Assignments and Classification of the Switch-2 Cluster and Neck/Neck Linker Conformations... 

Fig. 3. Conformation of the switch-2 cluster and neck linker/neck region in various members of the kinesin superfamily. The upper four panels (A, B, E, F) show crystal structures of N-type kinesins with their motor domain at the N-terminus and the neck at the C-terminus. (C), (D), (G), and (H) show C- and M-type kinesins with their neck N-terminal to the motor domain, except for PoKCBP (G) where the C-terminal neck mimic is shown instead of the N-terminal neck (which is not included in the crystal structure). Each structure is shown in two orientations that differ by a rotation of 90 degrees. Rat conventional kinesin (RnKHC [A]) has been chosen to define standard orientations with the neck helix a7 parallel/perpendicular to the drawing area. Orientations for the other structures have been determined by least-squares superposition of their P-loop regions with that of RnKHC (using 11 Ca-atoms of residues F83-T93 in RnKHC). (B), (C), and (D) show the structures of dimeric constructs with the second motor domain in pale colors. The Ned structure in (C) is 180-degree symmetric the symmetry axis is oblique to the drawing plane and coincides with the axis of the coiled-coil that is formed by the two neck helices. In the asymmetric structure of the Ned N600K mutant (D), the second motor domain (pale) is rotated by about 75 degrees around an axis perpendicular to the coiled-coil. The structures shown in (A), (B), (F), and (G) have their switch-2 cluster in permissive conformation, whereas the conformation of structures (C), (D), (E), and (H) is obstructive, as can be told by observing the slope of the extended switch-2 helix a4. Color code red, switch-2 cluster including the extended...

The motor domain of human Eg5 (HsKSP), a member of the kinesin-5 (formerly BimC) family, shares more than 40% identity with the kinesin-1 motor domain. The overall structure of an HsKSP construct of the first 368 amino acids (including 10 amino acids of the class-specific neck linker) complexed with ADP is very similar to the structure of kinesin-1 (PDB code 1116 Turner et al., 2001). The major differences are (1) an extension of the /Miairpin / lb-L2-/ lc in the N-terminal lobe ( L2 finger ) due to an insert of eight amino acids, (2) an enlargement of loop L5 between a2a and a2b by another insert of eight amino acids, (3) an elongation of loop L10 between / 6 and [17 at the tip of the core domain, and, most remarkably,... 

Turner, J., Anderson, R., Guo, J., Beraud, C., Fletterick, R., and Sakowicz, R. (2001). Crystal structure of the mitotic spindle kinesin Eg5 reveals a novel conformation of the neck-linker. / Biol. Chem. 276, 25496-25502. 

Figure 34.12. Neck Linker. A comparison of the structures of a kinesin bound to ADP and bound to an ATP analog. The neck linker (orange), which connects the head domain to the remainder of the kinesin molecule, is bound to the head domain in the presence of the ATP analog but is free in the presence of ADP only.

Figure 34.26. Structure of Ned. The head domain of ned is quite similar to that of conventional kinesin, including the presence of a P-loop NTPase domain (shaded in purple). In the ADP form of ned (shovm), the amino-terminal part of this fragment forms an a-helix that docks into the site occupied by the neck linker in the ATP form of conventional kinesin.

Figure 34.24 Krnesin moving along a microtubule. (1) One head of a two-headed kinesin molecule, initially with both heads in the ADP form, binds to a microtubule. (2) The release of ADP and the binding of ATP results in a conformational change that locks the head to the microtubule and pulls the neck linker (orange) to the head domain, throwing the second domain toward the plus end of the microtubule. (3) ATP undergoes hydrolysis while the second head interacts with the microtubule.

The structure of the kinesin monomer is classified into the three subdomains—head, neck-linker, and tail (see Figure I.IA). The head domain (residue 1-323) contains a nucleotide-binding pocket, a catalytic site, which controls the conformational state of the neck-linker (residue 324-338) made of 15 amino acids. The neck-helix domain (residues from 339 to the C-terminus), extended from the neck-linker, forms an alpha-helical structure dimeric kinesins are made via coiled-coil interactions between the neck-helices from two monomers (see Figure I.IA). 

FIGURE 1.1 (See color insert following page 172.) Kinesin and microtubule. (A) Conventional kinesins are homodimer, each of the monomer is made of head, neck-linker, and neck-helix domain. The neck-linkers of two heads are colored in green and yellow, respectively. The neck-helices from the two monomers associate the two subunits. (B) A microtubule with 13 protofilaments, each of which is made of an 8nm periodic head-to-taU alignment of the tubulin dimer subunits. A single protofilament that is used as a track for kinesin is colored in red. Kinesins take steps hand-over-hand along the protofilament. 

Binding Affinity between the Monomeric Kinesin and MT, and the Conformation of Neck-Linker with Varying Nucleotide State... 

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